Niema Moshiri, PhD

Assistant Teaching Professor
Department of Computer Science & Engineering
UC San Diego

Areas of Expertise: Computational viral epidemiology, phylogenetics, models of sequence and tree evolution, Massive Adaptive Interactive Text (MAIT) development

Tracking Viral Epidemics Course Spring 2021 - Lectures

Pekar J, Worobey M, Moshiri N, Scheffler K, Wertheim JO (2021). “Timing the SARS-CoV-2 Index Case in Hubei Province.” Science. 372(6540):412-417. doi:10.1126/science.abf8003

Keehner J, Horton LE, Binkin NJ, Laurent LC, Pride D, Longhurst CA, Abeles SR, Torriani FJ, SEARCH Alliance (Aigner S, Andersen KG, Anderson C, Baer NA, Barber T, Belda-Ferre P, Betty M, Birmingham A, Castro-Martinez A, Chac´on M, Cheung W, Crescini ES, De Hoff P, Eisner ER, Eisner ER, Fisch K, Vargas LF, Gangavarapu K, Hakim A, Henson B, Hobbs C, Humphrey G, Jepsen K, Kapadia BK, Knight R, Lastrella AL, Laurent LC, Lawrence ES, Machnicki M, Marotz CA, Matteson NL, Maunder DJ, Moshiri N, Ngo TT, Nouri A, Ostrander TR, Plascencia A, Ruiz CA, Salido RA, Sathe S, Seaver P, Smoot EW, Tsai R, Wu MY, Xia B, Yeo GW, Zeller M) (2021). “Resurgence of SARS-CoV-2 Infection in a Highly Vaccinated Health System Workforce.” The New England Journal of Medicine. doi:10.1056/NEJMc2112981

Moshiri N, Ragonnet-Cronin M, Wertheim JO, Mirarab S (2018). “FAVITES: simultaneous simulation of transmission networks, phylogenetic trees, and sequences.” Bioinformatics. 35(11):1852-1861. doi:10.1093/bioinformatics/bty921

Moshiri N (2020). “ViralMSA: Massively scalable reference-guided multiple sequence alignment of viral genomes.” Bioinformatics. 37(5):714-716. doi:10.1093/bioinformatics/btaa743

Salamat S, Moshiri N, Rosing T (2021). “FPGA Acceleration of Pairwise Distance Calculation for Viral Transmission Clustering.” IEEE Biomedical Circuits and Systems Conference (BioCAS) 2021. In press.

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